Identification of the CFTR c.1666A \u3e G mutation in hereditary inclusion body myopathy using next-generation sequencing analysis

Hereditary inclusion body myopathy (HIBM) is a rare autosomal recessive adult onset muscle disease which affects one to three individuals per million worldwide. This disease is autosomal dominant and occurs in adulthood. Our previous study reported a new subtype of HIBM linked to the susceptibility locus at 7q22.1-31.1. The present study is aimed to identify the candidate gene responsible for the phenotype in HIBM pedigree. After multipoint linkage analysis, we performed targeted capture sequencing on 16 members and whole-exome sequencing (WES) on 5 members. Bioinformatics filtering was performed to prioritize the candidate pathogenic gene variants, which were further genotyped by Sanger sequencing. Our results showed that the highest peak of LOD score (4.70) was on chromosome 7q22.1-31.1.We identified 2 and 22 candidates using targeted capture sequencing and WES respectively, only one of which as CFTRc.1666A \u3e G mutation was well cosegregated with the HIBM phenotype. Using transcriptome analysis, we did not detect the differences of CFTR\u27s mRNA expression in the proband compared with healthy members. Due to low incidence of HIBM and there is no other pedigree to assess, mutation was detected in three patients with duchenne muscular dystrophyn (DMD) and five patients with limb-girdle muscular dystrophy (LGMD). And we found that the frequency of mutation detected in DMD and LGMD patients was higher than that of being expected in normal population. We suggested that the CFTRc.1666A \u3e G may be a candidate marker which has strong genetic linkage with the causative gene in the HIBM famil

Application of Homozygosity Haplotype Analysis to Genetic Mapping with High-Density SNP Genotype Data

BACKGROUND: In families segregating a monogenic genetic disorder with a single disease gene introduction, patients share a mutation-carrying chromosomal interval with identity-by-descent (IBD). Such a shared chromosomal interval or haplotype, surrounding the actual pathogenic mutation, is typically detected and defined by multipoint linkage and phased haplotype analysis using microsatellite or SNP genotype data. High-density SNP genotype data presents a computational challenge for conventional genetic analyses. A novel non-parametric method termed Homozygosity Haplotype (HH) was recently proposed for the genome-wide search of the autosomal segments shared among patients using high density SNP genotype data. METHODOLOGY/PRINCIPAL FINDINGS: The applicability and the effectiveness of HH in identifying the potential linkage of disease causative gene with high-density SNP genotype data were studied with a series of monogenic disorders ascertained in eastern Canadian populations. The HH approach was validated using the genotypes of patients from a family affected with a rare autosomal dominant disease Schnyder crystalline corneal dystrophy. HH accurately detected the approximately 1 Mb genomic interval encompassing the causative gene UBIAD1 using the genotypes of only four affected subjects. The successful application of HH to identify the potential linkage for a family with pericentral retinal disorder indicates that HH can be applied to perform family-based association analysis by treating affected and unaffected family members as cases and controls respectively. A new strategy for the genome-wide screening of known causative genes or loci with HH was proposed, as shown the applications to a myoclonus dystonia and a renal failure cohort. CONCLUSIONS/SIGNIFICANCE: Our study of the HH approach demonstrates that HH is very efficient and effective in identifying potential disease linked region. HH has the potential to be used as an efficient alternative approach to sequencing or microsatellite-based fine mapping for screening the known causative genes in genetic disease study

The genetics of colored sequence synesthesia: Evidence of linkage to chromosome 16q and genetic heterogeneity for the condition

Synesthesia is a perceptual condition in which normal sensory stimulation can trigger anomalous sensory experiences. For example, synesthetes may experience colors in response to sounds, tastes in response to words, or smells in response to touch. We here focus on colored sequence synesthesia, in which color experiences are triggered by learned ordinal sequences such as letters, numbers, weekdays and months. Although synesthesia has been noted in the scientific literature for over a century, it is understood only at the level of the phenomenology, and not at the molecular and neural levels. We have performed a linkage analysis to identify the first genetic loci responsible for the increased neural crosstalk underlying colored sequence synesthesia. Our analysis has identified a 23 MB region on chromosome 16 as a putative locus for the trait. Our data provide the first step in understanding neural crosstalk from its molecular basis to its behavioral consequences, opening a new inroad into the understanding of the multisensory brain

Contribution of common and rare variants to bipolar disorder susceptibility in extended pedigrees from population isolates.

Current evidence from case/control studies indicates that genetic risk for psychiatric disorders derives primarily from numerous common variants, each with a small phenotypic impact. The literature describing apparent segregation of bipolar disorder (BP) in numerous multigenerational pedigrees suggests that, in such families, large-effect inherited variants might play a greater role. To identify roles of rare and common variants on BP, we conducted genetic analyses in 26 Colombia and Costa Rica pedigrees ascertained for bipolar disorder 1 (BP1), the most severe and heritable form of BP. In these pedigrees, we performed microarray SNP genotyping of 838 individuals and high-coverage whole-genome sequencing of 449 individuals. We compared polygenic risk scores (PRS), estimated using the latest BP1 genome-wide association study (GWAS) summary statistics, between BP1 individuals and related controls. We also evaluated whether BP1 individuals had a higher burden of rare deleterious single-nucleotide variants (SNVs) and rare copy number variants (CNVs) in a set of genes related to BP1. We found that compared with unaffected relatives, BP1 individuals had higher PRS estimated from BP1 GWAS statistics (P = 0.001 ~ 0.007) and displayed modest increase in burdens of rare deleterious SNVs (P = 0.047) and rare CNVs (P = 0.002 ~ 0.033) in genes related to BP1. We did not observe rare variants segregating in the pedigrees. These results suggest that small-to-moderate effect rare and common variants are more likely to contribute to BP1 risk in these extended pedigrees than a few large-effect rare variants

Phenotypic heterogeneity and genetic modification of P102L inherited prion disease in an international series

The largest kindred with inherited prion disease P102L, historically Gerstmann-Sträussler-Scheinker syndrome, originates from central England, with émigrés now resident in various parts of the English-speaking world. We have collected data from 84 patients in the large UK kindred and numerous small unrelated pedigrees to investigate phenotypic heterogeneity and modifying factors. This collection represents by far the largest series of P102L patients so far reported. Microsatellite and genealogical analyses of eight separate European kindreds support multiple distinct mutational events at a cytosine-phosphate diester-guanidine dinucleotide mutation hot spot. All of the smaller P102L kindreds were linked to polymorphic human prion protein gene codon 129M and were not connected by genealogy or microsatellite haplotype background to the large kindred or each other. While many present with classical Gerstmann-Sträussler-Scheinker syndrome, a slowly progressive cerebellar ataxia with later onset cognitive impairment, there is remarkable heterogeneity. A subset of patients present with prominent cognitive and psychiatric features and some have met diagnostic criteria for sporadic Creutzfeldt-Jakob disease. We show that polymorphic human prion protein gene codon 129 modifies age at onset: the earliest eight clinical onsets were all MM homozygotes and overall age at onset was 7 years earlier for MM compared with MV heterozygotes (P = 0.02). Unexpectedly, apolipoprotein E4 carriers have a delayed age of onset by 10 years (P = 0.02). We found a preponderance of female patients compared with males (54 females versus 30 males, P = 0.01), which probably relates to ascertainment bias. However, these modifiers had no impact on a semi-quantitative pathological phenotype in 10 autopsied patients. These data allow an appreciation of the range of clinical phenotype, modern imaging and molecular investigation and should inform genetic counselling of at-risk individuals, with the identification of two genetic modifiers

Forensic Genealogy: A Tool in DNA Analysis

DNA is the basic unit of which differentiates one individual to the next. Short Tandem Repeats and Single Nucleotide Polymorphisms are two locations of DNA that have been the most successful in DNA analysis. Unique DNA profiles can be created so that interpretations can be made about the individual who contributed to the DNA sample. Systems like STRmix are currently being employed to give unbiased assumptions about the DNA profiles. There are several different statistical approaches in assigning probabilities to DNA evidence, likelihood ratio and random match probability are two common approaches. After assumptions are made, comparisons can be made between DNA profiles to find related familial members due to similarities in DNA profiles. Maternal kinship can be considered based on the mitochondrial DNA while paternal kinship is based on the inheritance of the Y chromosome. The Golden State Killer was a famous case that opened the door of applying forensic genetics and consumer genealogy sites to investigations. The future of forensic genealogy is endless, but first policies must be put out in place to protect the privacy of individuals DN

The genetic basis of fitness: detecting inbreeding depression and selective sweeps in bighorn sheep

Understanding the fitness effects of inbreeding is a crucial and long standing goal in conservation and evolutionary biology. Many studies measure individual inbreeding (F, the proportion of genome that is identical by descent) and its fitness effects using either pedigrees or molecular markers. Knowing which genes most strongly affect fitness can help to explain why some individuals outperform others, and elucidate the mechanisms of inbreeding depression and adaptation. However, identifying adaptive genes is difficult in most species because of limited genomic resources. I used simulations to evaluate the performance of marker- and pedigree-based measures of F and inbreeding depression. I found that FP was less precise than marker-based measures of F in a broad range of scenarios. For example, the true F was always more strongly correlated with heterozygosity measured with 5000 single nucleotide polymorphisms (SNPs) than with FP. F was also more strongly correlated with the proportion of the genome in long runs of homozygosity (FROH, estimated with 35K SNPs) than with FP. I also show that heterozygosity-based estimates of the strength of inbreeding depression are precise in populations with high variance in F (e.g., σ2(F) ≥ 0.002). A potential solution to the imprecision of FP is to use genetic markers to correct for the kinship of pedigree founders. However, I found that founder kinship-corrected values of FP were also imprecise. These results show that F and inbreeding depression can be most reliably measured with genetic markers in most scenarios – countering the prevailing historical view that F is most reliably measured with pedigrees. I used whole genome sequences of pooled DNA aligned to the domestic sheep genome to detect candidate adaptive genes in bighorn sheep. I detected selection signatures in 53 genomic regions containing genes. However, simulations suggest that some of these selection signatures may be false positives. Putatively selected genomic regions contained genes involved with traits known to affect fitness in bighorn sheep (e.g., horn and body growth). These results provide candidate genes for traits known to strongly influence fitness in bighorn, and illustrate the great promise of WGS for detecting selection signatures in small populations

Germline mutations in MAP3K6 are associated with familial gastric cancer

Gastric cancer is among the leading causes of cancer-related deaths worldwide. While heritable forms of gastric cancer are relatively rare, identifying the genes responsible for such cases can inform diagnosis and treatment for both hereditary and sporadic cases of gastric cancer. Mutations in the E-cadherin gene, CDH1, account for 40% of the most common form of familial gastric cancer (FGC), hereditary diffuse gastric cancer (HDGC). The genes responsible for the remaining forms of FGC are currently unknown. Here we examined a large family from Maritime Canada with FGC without CDH1 mutations, and identified a germline coding variant (p.P946L) in mitogen-activated protein kinase kinase kinase 6 (MAP3K6). Based on conservation, predicted pathogenicity and a known role of the gene in cancer predisposition, MAP3K6 was considered a strong candidate and was investigated further. Screening of an additional 115 unrelated individuals with non-CDH1 FGC identified the p.P946L MAP3K6 variant, as well as four additional coding variants in MAP3K6 (p.F849Sfs*142, p.P958T, p.D200Y and p.V207G). A somatic second-hit variant (p.H506Y) was present in DNA obtained from one of the tumor specimens, and evidence of DNA hypermethylation within the MAP3K6 gene was observed in DNA from the tumor of another affected individual. These findings, together with previous evidence from mouse models that MAP3K6 acts as a tumor suppressor, and studies showing the presence of somatic mutations in MAP3K6 in non-hereditary gastric cancers and gastric cancer cell lines, point towards MAP3K6 variants as a predisposing factor for FGC.The following agencies provided funding for this project: Genome Canada, Genome Atlantic, Nova Scotia Health Research Foundation, Nova Scotia Research and Innovation Trust, Dalhousie Faculty of Medicine, Dalhousie Department of Ophthalmology, Health Canada, The Centre for Drug Research and Development, Capital District Health Authority, IWK Health Centre Foundation, Capital Health Research Fund, and The COMPETE/FEDER Portuguese Foundation for Science and Technology (FCT), Projects Ref. FCT PTDC/SAU-GMG/110785/2009 and Post-doc grant SFRH/BPD/79499/2011 to HP “financiados no âmbito do Programa Operacional Temático Factores de Competitividade (COMPETE) e comparticipado pelo fundo Comunitário Europeu FEDER.” MES is supported by the CHU Ste-Justine Centre de Recherche. The authors would like to acknowledge the contribution of: the Genome Quebec High Throughput Sequencing Platform; and Sónia Sousa and José Carlos Machado from the IPATIMUP Diagnostics Unit, Porto, Portugal. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript